Once my student taking AGH635. Molecular and Cellular Analysis in Plant Breeding Course raised the following case: “I have collected 200 accessions of plants randomly collected from 20 different provinces in Indonesia. The accessions were brought to and evaluated in Bogor for their resistance against certain plant disease. In the evaluation, 50 accessions were scored as susceptible and 150 accessions were resistance. Moreover, I also analyzed the accessions using 100 loci of SSR markers. All of the SSR marker loci were polymorphic for the accessions.”
The student than asked me the following questions:
- The disease response data indicate the presence of a 3:1 ratio between resistance (“R”)and susceptible (“r”) phenotypes, respectively. Does this mean a single gene (a single locus) is controlling the resistance phenotype ?
- If by analyzing both the SSR markers and the resistance phenotype data, I am able to identify a number of markers are always present in the resistance plants (i.e. the resistance plant always carry certain SSR markers), is it correct to say that I can use those markers as indirect selection indicators for the resistant plants (carrying the R gene)? In other word, are the identified markers linked to the R locus?
My answers to those questions are as follow:
Q.1. The fact that the 3:1 ratio between resistant vs. susceptible plants does not necessary guarantee a single gene (a single locus) controls the resistance phenotype. The idea of 3:1 ratio as a segregation ratio of a single gene (single locus) came from the Mendelian law of segregation (as illustrated in Figure 1 below). In the Mendelian law of segregation, hybridization between two homozygous parents (i.e. P1 and P2) result in heterozygous F1 and hybridization between heterozygous F1 result in a segregated F2 population as illustrated in the Figure 1.
Let’s consider the R locus with “R” and “r” alleles. The “R” allele is responsible for resistance character and the “r” for the susceptible one, respectively. In the segregated F2 population, the ratio of resistance vs. susceptible plants would be 3:1. In such case, the 3:1 ratio of R:r indicate the segregation of a single locus.
However, in the case that the student’s raised, the population in question was not derived from hybridization between two common parents (the population was not descended from common parents). Therefore, it is not a segregated population and as such the 3:1 ratio between resistance and susceptible phenotypes does not mean anything. The Mendelian law of segregation does not apply in the population in question. Even if one observes a 3:1 ratio, it does not necessarily indicate the presence of a single segregating locus.
Q.2. To reiterate the case: one observed the coincidence between the resistance character and the presence of SSR markers (i.e. plants that are resistance, also carry selected SSR markers). Was this an indication of a linkage between the R and the SSR markers loci? The answer to such question is not necessarily correct to say that the loci are linked based on such observations. Let’s consider the following illustration (Figure 2):
Based on their phenotype, the two plants (i.e. Plant A and B) as illustrated in Figure 2 are both scored as resistance and (+) for M marker. However, if one consider the genotype of the two plants, the resistance character in Plant A is controlled by R1 locus in chromosome #1 while in Plant B is by R2 locus in chromosome #2. In Figure 2, the R1 locus is in the same chromosome as the M locus (i.e. they both reside in chromosome #1) while the R2 locus (chromosome #2) is not in the same locus as the M locus (chromosome #1).
Since the accessions in the population are not descended from the same parents, there is no guarantee that the resistance phenotype is actually controlled by the same R gene/locus. Therefore, it is not valid to conclude that the resistance phenotype is actually linked to the SSR markers loci based on such data. To be able to conclude the presence of linkage between two loci, one need to have different sets of data, such as: segregated data from a population descended from common parents (common by descend).
- If the population is not descended from common parents (common by descend), the Mendelian segregation ratio would not apply and can not be used to estimate number of segregating loci
- Even if one observed the presence of correlated phenotypes (i.e. the resistance and the marker M are both presence in the majority of the accessions, it is not necessarily indicate that the two loci are linked or existed in the same chromosome.
- To be able to estimate the number of genes/loci controlling a phenotype by estimating segregation ratio of the phenotypes, one need to use a population descended from the same/common parents (common by descend). Similarly, to be able to determine whether two loci are segregating independently or linked in a single chromosome, one need to have a population descended from the same parents (common by descend).